5VLR

CRYSTAL STRUCTURE OF PI3K DELTA IN COMPLEX WITH A TRIFLUORO-ETHYL-PYRAZOL-PYROLOTRIAZINE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.279 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9EMClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Identification of a Potent, Selective, and Efficacious Phosphatidylinositol 3-Kinase delta (PI3K delta ) Inhibitor for the Treatment of Immunological Disorders.

Liu, Q.Shi, Q.Marcoux, D.Batt, D.G.Cornelius, L.Qin, L.Y.Ruan, Z.Neels, J.Beaudoin-Bertrand, M.Srivastava, A.S.Li, L.Cherney, R.J.Gong, H.Watterson, S.H.Weigelt, C.Gillooly, K.M.McIntyre, K.W.Xie, J.H.Obermeier, M.T.Fura, A.Sleczka, B.Stefanski, K.Fancher, R.M.Padmanabhan, S.Rp, T.Kundu, I.Rajareddy, K.Smith, R.Hennan, J.K.Xing, D.Fan, J.Levesque, P.C.Ruan, Q.Pitt, S.Zhang, R.Pedicord, D.Pan, J.Yarde, M.Lu, H.Lippy, J.Goldstine, C.Skala, S.Rampulla, R.A.Mathur, A.Gupta, A.Arunachalam, P.N.Sack, J.S.Muckelbauer, J.K.Cvijic, M.E.Salter-Cid, L.M.Bhide, R.S.Poss, M.A.Hynes, J.Carter, P.H.Macor, J.E.Ruepp, S.Schieven, G.L.Tino, J.A.

(2017) J Med Chem 60: 5193-5208

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00618
  • Primary Citation of Related Structures:  
    5VLR

  • PubMed Abstract: 

    PI3Kδ plays an important role controlling immune cell function and has therefore been identified as a potential target for the treatment of immunological disorders. This article highlights our work toward the identification of a potent, selective, and efficacious PI3Kδ inhibitor. Through careful SAR, the successful replacement of a polar pyrazole group by a simple chloro or trifluoromethyl group led to improved Caco-2 permeability, reduced Caco-2 efflux, reduced hERG PC activity, and increased selectivity profile while maintaining potency in the CD69 hWB assay. The optimization of the aryl substitution then identified a 4'-CN group that improved the human/rodent correlation in microsomal metabolic stability. Our lead molecule is very potent in PK/PD assays and highly efficacious in a mouse collagen-induced arthritis model.


  • Organizational Affiliation

    Research & Development, Bristol-Myers Squibb Company , Route 206 and Province Line Road, Princeton, New Jersey 08543, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform1,013Homo sapiensMutation(s): 0 
Gene Names: PIK3CD
EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00329 (Homo sapiens)
Explore O00329 
Go to UniProtKB:  O00329
PHAROS:  O00329
GTEx:  ENSG00000171608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00329
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha170Homo sapiensMutation(s): 4 
Gene Names: PIK3R1GRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9EM
Query on 9EM

Download Ideal Coordinates CCD File 
C [auth A]4-acetyl-1-(3-{4-amino-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazol-5-yl]pyrrolo[2,1-f][1,2,4]triazin-7-yl}phenyl)-3,3-dimethylpiperazin-2-one
C25 H25 F3 N8 O2
KSAKMNJFOKNIAA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9EM BindingDB:  5VLR IC50: min: 3, max: 71 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.279 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.847α = 90
b = 108.579β = 90
c = 142.734γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 9EMClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2017-06-07 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references